REPORTE DE MUESTRA
- Nombre
- Thalassomics
- Contacto
- info@thalassomics.com
- Sitio Web
- https://github.com/trippv/integrity_massively
- Tipo de proyecto
- RNA-seq
- Platafora
- HiSeq 2500 High Output V4
- Setup
- 2x125
General Statistics
| Sample Name | % Duplication | % > Q30 | Mb Q30 bases | Reads After Filtering | GC content | % PF | % Adapter | Error rate | Non-primary | Reads mapped | % Mapped | % Proper pairs | % MapQ 0 reads | Total seqs | Mean insert | % Aligned |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| batch1 | 0.16% | 0.0M | 0.1M | 99.9% | 99.2% | 0.0% | 0.1M | 167.6bp | 99.9% | |||||||
| batch1_chrI | 0.0% | 92.8% | 7.6Mb | 0.1M | 43.4% | 99.4% | 1.5% | |||||||||
| batch2 | 0.15% | 0.0M | 0.1M | 99.9% | 99.4% | 0.0% | 0.1M | 172.8bp | 99.9% | |||||||
| batch2_chrI | 0.0% | 92.9% | 10.6Mb | 0.1M | 43.4% | 100.0% | 0.6% | |||||||||
| batch3 | 0.16% | 0.0M | 0.1M | 99.9% | 99.3% | 0.0% | 0.1M | 168.8bp | 99.8% | |||||||
| batch3_chrI | 0.0% | 92.8% | 8.1Mb | 0.1M | 43.6% | 99.5% | 1.4% | |||||||||
| chem1 | 0.26% | 0.0M | 0.1M | 99.9% | 98.9% | 0.0% | 0.1M | 166.1bp | 99.9% | |||||||
| chem1_chrI | 0.0% | 92.9% | 6.7Mb | 0.1M | 43.4% | 100.0% | 0.7% | |||||||||
| chem2 | 0.25% | 0.0M | 0.1M | 99.9% | 99.0% | 0.0% | 0.1M | 172.7bp | 99.9% | |||||||
| chem2_chrI | 0.0% | 93.1% | 8.4Mb | 0.1M | 43.3% | 100.0% | 0.5% | |||||||||
| chem3 | 0.25% | 0.0M | 0.1M | 99.9% | 99.1% | 0.0% | 0.1M | 172.3bp | 99.9% | |||||||
| chem3_chrI | 0.0% | 93.1% | 10.1Mb | 0.1M | 43.4% | 100.0% | 0.6% |
fastp
0.23.4
All-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...).URL: https://github.com/OpenGene/fastpDOI: 10.1093/bioinformatics/bty560
Fastp goes through fastq files in a folder and perform a series of quality control and filtering. Quality control and reporting are displayed both before and after filtering, allowing for a clear depiction of the consequences of the filtering process. Notably, the latter can be conducted on a variety of parameters including quality scores, length, as well as the presence of adapters, polyG, or polyX tailing.Filtered Reads
Filtering statistics of sampled reads.
Insert Sizes
Insert size estimation of sampled reads.
Sequence Quality
Average sequencing quality over each base of all reads.
GC Content
Average GC content over each base of all reads.
N content
Average N content over each base of all reads.
Samtools
1.20
HTSlib:
1.21
Toolkit for interacting with BAM/CRAM files.URL: http://www.htslib.orgDOI: 10.1093/bioinformatics/btp352
Percent mapped
Alignment metrics from samtools stats; mapped vs. unmapped reads vs. reads mapped with MQ0.
For a set of samples that have come from the same multiplexed library, similar numbers of reads for each sample are expected. Large differences in numbers might indicate issues during the library preparation process. Whilst large differences in read numbers may be controlled for in downstream processings (e.g. read count normalisation), you may wish to consider whether the read depths achieved have fallen below recommended levels depending on the applications.
Low alignment rates could indicate contamination of samples (e.g. adapter sequences), low sequencing quality or other artefacts. These can be further investigated in the sequence level QC (e.g. from FastQC).
Reads mapped with MQ0 often indicate that the reads are ambiguously mapped to multiple locations in the reference sequence. This can be due to repetitive regions in the genome, the presence of alternative contigs in the reference, or due to reads that are too short to be uniquely mapped. These reads are often filtered out in downstream analyses.
Alignment stats
This module parses the output from samtools stats. All numbers in millions.
Bowtie 2 / HiSAT2
Results from both Bowtie 2 and HISAT2, tools for aligning reads against a reference genome.URL: http://bowtie-bio.sourceforge.net/bowtie2; https://ccb.jhu.edu/software/hisat2DOI: 10.1038/nmeth.1923; 10.1038/nmeth.3317; 10.1038/s41587-019-0201-4
Paired-end alignments
This plot shows the number of reads aligning to the reference in different ways.
There are 6 possible types of alignment:
- PE mapped uniquely: Pair has only one occurence in the reference genome.
- PE mapped discordantly uniquely: Pair has only one occurence but not in proper pair.
- PE one mate mapped uniquely: One read of a pair has one occurence.
- PE multimapped: Pair has multiple occurence.
- PE one mate multimapped: One read of a pair has multiple occurence.
- PE neither mate aligned: Pair has no occurence.
GffCompare
0.12.9
Tool to compare, merge and annotate one or more GFF files with a reference annotation in GFF format.URL: https://ccb.jhu.edu/software/stringtie/gffcompare.shtmlDOI: 10.12688/f1000research.23297.1
Accuracy values
Displayed are the accuracy values precisiond and sensitivity for different levels of genomic features. The metrics are calculated for the comparison of a query and reference GTF file.
Accuracy metrics are calculated as described in Burset et al. (1996). Sensitivity is the true positive rate, Precision True Positives are query features that agree with features in the reference. The exact definition depends on the feature level:
- Base: True positives are bases reported at the same coordinates.
- Exon: Comparison units are exons that overlap in query and reference with same coordinates.
- Intron chain: True positives are query transcripts for which all introns coordinates match those in the reference.
- Transcript: More stringent then intron chain, all Exon coordinates need to match. Outer exon coordinates (start + end) can vary by 100 bases in default settings
- Locus: Cluster of exons need to match.
A more in depth description can be found here.
Novel features
Number of novel features, present in the query data but not found in the reference annotation.
Missing features
False negative features, which are found in the reference annotation but missed (not present) in the query data.
Pca Plot
Análisis de Expresión Diferencial
PCA de expresión génica
El gráfico de PCA (Análisis de Componentes Principales) permite visualizar cómo se agrupan las muestras según su perfil de expresión génica. Muestras cercanas entre sí tienen patrones de expresión similares, lo que puede reflejar similitudes biológicas o técnicas entre los grupos.
Expresión diferencial
El volcano plot muestra los genes diferencialmente expresados entre dos grupos. Cada punto representa un gen: el eje X indica el cambio en la expresión (log₂ Fold Change), y el eje Y indica la significancia estadística (-log₁₀ p-valor ajustado). Los genes más alejados y en rojo son los más significativamente regulados.
Software Versions
Software Versions lists versions of software tools extracted from file contents.
| Group | Software | Version |
|---|---|---|
| GffCompare | GffCompare | 0.12.9 |
| Samtools | HTSlib | 1.21 |
| Samtools | 1.20 | |
| fastp | fastp | 0.23.4 |
